Gluconeogenesis happens in the liver primarily, and secondarily in the kidneys. The glucose will enter circulation, and some of that, presumably, will get to the GI tract, but not on the lumen side where the bacteria would be colonizing.

Umm, most bacteria do not make spores. Only some gram positive species, typically soil dwellers like Bacillus or Streptomyces. Or some bugs like Clostridium. Most of your probiotic species don't make spores. Now bacteria have all sorts of other strategies for coping with starvation, but spore forming is only found in a few genera. Also, we really don't know squat about the microbial ecology of the gut. 2-4 member microbial communities in homogeneous environments in test tubes are ridiculously complex. The gut is another beast altogether.

And I agree with Bill, that some of the population 'might' die off. You won't be eating any soluble fiber for them to chow down on. Though bacteria are resourceful little beings that I'm sure could survive for a good amount of time (while you fast) without dying (Source: Microbiology course*). From an adaption standpoint of early human beings, it wouldn't seem right for a good amount of the beneficial gut flora to die during an extended period without food ... would it? Just speculation from me though.

*if you'd like me to find the book title just let me know and I'll try to find it

the 'fasting' mentioned in the study was merely a reduced calorie diet consisting of fruit juice and vegetable soup. This would be very unlikely to significantly change the gut flora over an eight day period.

If you look up 'bacterial sporulation' you will find that many bacteria, when they have run out of food, will 'select' a few of their numbers to undergo sporulation (colony sporulation factor), and these spores are very stable over time and in varying acidities, 'waiting' for the right conditions to come back.
Sporulation is used by some probiotics as a way to make sure that the desired strains make it through the stomach acid so that they might better colonize the intestines.

as RG73 points out, only some bacteria
do this, but there are many ways for
bacteria to survive for extended
periods. DIG INTO http://en.wikipedia.org/wiki/Gut_flora for more details on huge variety.

The Arthur Andrew site says it pretty well while promoting their high-end probiotic Syntol:

Spore germination is a dependable
means of delivering healthy flora to
the intestine in less than ideal
conditions. Most bacteria are
susceptible to any acidic pH range,
mainly thriving in the more alkaline
lower GI, but spores are able to
withstand a broader range of variables
in regards to pH and temperature
ranges. This improves the chances
that the probiotic strain will
properly germinate and begin the
process of restoring intestinal
balance.

Umm, most bacteria do not make spores. Only some gram positive species, typically soil dwellers like Bacillus or Streptomyces. Or some bugs like Clostridium. Most of your probiotic species don't make spores. Now bacteria have all sorts of other strategies for coping with starvation, but spore forming is only found in a few genera. Also, we really don't know squat about the microbial ecology of the gut. 2-4 member microbial communities in homogeneous environments in test tubes are ridiculously complex. The gut is another beast altogether.

First, a 2009 to set the stage-- http://aem.asm.org/content/75/20/6451.full#content-block discusses the impact of fasting (on hamsters) on proportions of gut-bacteria. Of interest is the fact that Akkermansia muciniphila survives fasting at a proportionally higher rate than other bacteria.

Questions I have that were not clarified in the first article is what is considered to be a "fast." Hamsters are not people; their metabolisms are capable of going through hibernation, but unlike humins, they don't have a huge amount of body-mass to burn through. So the translation, if any, to humin feeding patterns is unclear. I do not know if there was follow-up to that question in a future study.

In Jared Diamond's latest book, "The World Before Yesterday," he makes the observation that wild / traditional humin beings did not tend to have frequent, small meals--they were often forced to fast every few days, when hunting or harvesting fell short. Other information I've read talks about the impact of antibiotics on increasing the bacteria that facilitate carbohydrate digestion in feedlot animals. My conclusion--sorry, the two articles I offered are all I have the umph to collect!--is that the near-continuous exposure to antibiotics that I experienced as a child are likely related to a die-off of those bacteria most likely to maintain a lean body, and also that a weekly fasting day may be beneficial in encouraging an increase in the gut-bacteria which are more common in those humins without excess body fat.

I have read that they pretty much stay the same, you might have a little bit of die off in population but the specific species and their proportions generally stay the same and will feed off the glucose you create from your own protein.

Gluconeogenesis happens in the liver primarily, and secondarily in the kidneys. The glucose will enter circulation, and some of that, presumably, will get to the GI tract, but not on the lumen side where the bacteria would be colonizing.